| CDII |
| ID: | 1452520386 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 60 (60) | ||
| Sequences: | 88 (41.7) | ||
| Seq/Len: | 1.467 | ||
| Nf(neff/√len): | 5.4 |
Jackhmmer Results: (2015_08)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.467).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 14_I | 19_S | 1.609 | 0.90 |
| 4_I | 12_K | 1.594 | 0.90 |
| 9_W | 34_W | 1.452 | 0.83 |
| 34_W | 41_I | 1.449 | 0.83 |
| 7_N | 46_E | 1.427 | 0.82 |
| 5_V | 25_V | 1.426 | 0.82 |
| 13_L | 19_S | 1.390 | 0.79 |
| 23_K | 28_Y | 1.373 | 0.78 |
| 7_N | 59_L | 1.355 | 0.77 |
| 6_G | 59_L | 1.334 | 0.75 |
| 37_K | 42_K | 1.311 | 0.73 |
| 34_W | 44_K | 1.297 | 0.72 |
| 36_C | 54_V | 1.277 | 0.71 |
| 14_I | 18_L | 1.272 | 0.70 |
| 8_P | 24_P | 1.237 | 0.67 |
| 23_K | 59_L | 1.212 | 0.65 |
| 23_K | 51_S | 1.204 | 0.64 |
| 24_P | 56_V | 1.202 | 0.64 |
| 29_P | 37_K | 1.192 | 0.63 |
| 9_W | 21_L | 1.190 | 0.63 |
| 28_Y | 31_T | 1.148 | 0.59 |
| 16_K | 38_L | 1.129 | 0.57 |
| 10_D | 34_W | 1.093 | 0.53 |
| 11_D | 26_S | 1.090 | 0.53 |
| 26_S | 38_L | 1.090 | 0.53 |
| 9_W | 44_K | 1.077 | 0.51 |
| 29_P | 48_Q | 1.065 | 0.50 |
| 6_G | 32_F | 1.064 | 0.50 |
| 37_K | 48_Q | 1.046 | 0.48 |
| 41_I | 54_V | 1.035 | 0.47 |
| 35_Q | 47_F | 1.033 | 0.47 |
| 17_L | 36_C | 1.022 | 0.46 |
| 7_N | 32_F | 1.011 | 0.45 |
| 28_Y | 38_L | 1.008 | 0.44 |
| 23_K | 54_V | 1.008 | 0.44 |
| 3_F | 31_T | 1.004 | 0.44 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4qpmA | 2 | 0.9167 | 98.8 | 0.605 | Contact Map |
| 2vdwB | 4 | 0.5833 | 4.5 | 0.921 | Contact Map |
| 4yczA | 1 | 0.6167 | 3 | 0.928 | Contact Map |
| 2od0A | 2 | 0.5667 | 2.9 | 0.928 | Contact Map |
| 2a33A | 2 | 0.2833 | 2.6 | 0.929 | Contact Map |
| 4ab7A | 8 | 0.8167 | 2.6 | 0.929 | Contact Map |
| 3hrlA | 1 | 0.6333 | 2.3 | 0.932 | Contact Map |
| 1pxvA | 2 | 0.65 | 2.2 | 0.932 | Contact Map |
| 3gqhA | 3 | 0.55 | 2.1 | 0.933 | Contact Map |
| 3pivA | 2 | 0.9833 | 2 | 0.934 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)